Additional file 4 of Extensive evaluation of ATAC-seq protocols for native or formaldehyde-fixed nuclei

Additional file 4: Supplementary Table S4. Hypergeometric tests. Column 1 (“TF”) indicates the name and source, if provided, of transcription factors. Columns 2 and 3 show the p value and adjusted p value calculated by Benjamini & Hochberg method. Column 4 indicates the fold enrichment. Column 5 shows the number of condition-specific “missing” peaks overlapping with each ChIP-seq data. Column 6 shows the number of “missing” ATAC-seq peaks in each condition. Column 7 indicates the number of background peaks overlapping with each ChIP-seq data. Column 8 shows the total number of background peaks for either native or fixed samples. Column 9 shows the number of ChIP-seq peaks. Columns 10-13 indicate the fixation state, buffer, temperature, and Tn5 enzyme, respectively. The “missing” ATAC-seq peaks were defined as the peaks that were observed in at least three other conditions, but not observed in the condition of interest. The background peaks indicate the peaks shared among at least three conditions and calculated separately for native and fixed samples. The fold enrichment for overlap with each ChIP-seq dataset was calculated by dividing the frequency of ATAC-seq peaks overlapped by ChIP-seq peaks observed in each condition (the ratio of Column 5 to Column 6) by the frequency of ATAC-seq peaks overlapped by ChIP-seq peaks observed in the background peak set (the ratio of Column 7 to Column 8).

附加文件 4：补充表 S4。超几何检验。第一列（“TF”）表示转录因子的名称及其来源（如有）。第二列和第三列展示了通过 Benjamini & Hochberg 方法计算得到的 p 值和调整后的 p 值。第四列表明了富集倍数。第五列显示了与每个 ChIP-seq 数据重叠的条件特异性“缺失”峰的数量。第六列展示了每个条件下“缺失”的 ATAC-seq 峰的数量。第七列表明了与每个 ChIP-seq 数据重叠的背景峰的数量。第八列显示了原始或固定样本的背景峰总数。第九列显示了 ChIP-seq 峰的数量。第十至第十三列分别表示固定状态、缓冲液、温度和 Tn5 酶。所谓的“缺失”ATAC-seq 峰是指至少在三种其他条件下观察到，但在感兴趣的条件中未观察到的峰。背景峰是指至少在三种条件下共享的峰，并在原始和固定样本中分别计算。重叠于每个 ChIP-seq 数据集的富集倍数通过将每个条件下观察到的 ATAC-seq 峰与 ChIP-seq 峰重叠的频率（第五列与第六列的比率）除以背景峰集中观察到的 ATAC-seq 峰与 ChIP-seq 峰重叠的频率（第七列与第八列的比率）来计算。